What a great question. One of the most common remarks I make on manuscripts relates to weaving more threads through the book (which really means, keeping track of your threads).
Novels in progress can be overly ego-centric via the main character, with secondary characters standing around like hand-maidens ready to serve. This can create both a claustrophobic atmosphere and a one-note plot. So grabbing hold of secondary characters' plots threads and pulling them through creates texture and interest.
Of course, there are other kinds of threads: character, metaphoric, thematic. These are as important as the plot threads. What I've been noticing lately is how good sit-coms are at repeating small details to a large effect. I was just discussing with my daughter Isabelle the Seinfeld episode where Elaine breaks up with her boyfriend and he calls her Bighead. She finds the comment ridiculous, but when she goes outside, birds keep flying into her head. A passer-by comments on how the birds just can't seem to avoid her. On a recent HBO sit-com, the boss is upset that a girl at work is exposing her midriff. When he tells her not to, she accuses him of calling her fat. There are several other scenes with the boss feeling politically incorrect about weight and women because of his faux pas, each increasing in hilarity because of the echo, with the viewer happily connecting the dots. The show ends with him falling off of a building and grabbing his employee's bared stomach fat to hang on for dear life.
On the opposite hand, I've recently seen two shows where the script opened up all kinds of plot threads and then just let them drop. The first was the new Spiderman musical on Broadway. The second was the film Black Swan which was "full of sound and fury, Signifying nothing," although probably not "told by an idiot" as the line from Macbeth begins. Both had these and-then-they-woke -up-and-it-was-all-a-dream type of endings. I wanted to jump up and yell: "But what about those threads!"
The thing I find most helpful for keeping track is to simply bold words on my computer draft that I want to pick up later. It might be a simple character detail, like nail biting, that I want to remember so I don't show the character later peeling off stamps with her long fingernails (consistency of character). Or maybe everyone in the surreal high pressure school bites their fingernails (thematic thread) or rebels against the demands of beauty (metaphor/theme), or she decides to be a hand model and needs to stop, but can't so she goes to a twelve step program where she meets the girl or man or dog or scissors of her dreams and lives happily ever after (plot thread). Any technique that notices the opportunities in front of us on the page will work. One book I can think of that does this brilliantly on every level is Holes. Other techniques/thoughts?